Intertidal mudflats are ecosystems submitted to natural hydrodynamical forcings during each tide. When the offshore water flows at high tide, a proportion of the biofilm produced at low tide can be resuspended in the water column and interact with the pelagic food web. As a consequence, the resuspension creates a link between the benthos and the pelagos, modifying their properties and the stability of the meta-ecosystem they form together. The aim of this study is to describe the consequences of the microbial biofilm resuspension on the pelagic food web, and to investigate the question of the stability of the benthos–pelagos coupling resulting from the biofilm resuspension. Two food webs were considered, corresponding to different hydrodynamical conditions in summer condition: one allowing the biofilm massive resuspension, and one without resuspension, but with particle sedimentation. The Monte-Carlo Markov Chain Linear Modelling was used to estimate the unknown flows of the food web. The comparison of the Ecological Network Analysis indices for the two food webs allowed defining their respective differences of structure and functioning. The results showed that the massive resuspension of the microbial biofilm stimulates pelagic primary production and microbial food web via a higher bacterivory. The higher activity of the whole system coupled with both a drop in the specialisation of the trophic pathways and a low cycling activity demonstrated that when massive resuspension occurs, the system is disturbed. In contrast, when sedimentation occurs, the food webs show functioning features pointing out to a higher stability of the whole system.